"I think it will hurt the results," Khosrowshahi told CNBC's "Squawk on the Street" on Monday. "But right now what we're worried about is making sure that our customers are okay. We're in this for the long game."

He added: "So, a couple of million dollars hurting a quarter is not going to throw off our long-term plans. I don't even have an estimate right now."

(Read More: US Airlines Cancel Flights, Hotels Book Up Before Hurricane)

Call Volume Doubles Amid Sandy

The immediate priority is managing travel fallout from Hurricane Sandy. Expedia has staffed up call centers, and call volume has been double normal capacity. Expedia is working with partners to reaccommodate guests as much as possible, he said. "It's all hands on deck," said Khosrowshahi, as many flights have been cancelled and travelers have been bumped.

"There are a lot of unhappy customers, just because of the situation, and what we try to do is make it better for them," he said.

Looking beyond Hurricane Sandy's impact, Khosrowshahi said the fastest growing part of their business is international, especially in Asia. "China, for example, is growing incredibly quickly for us," he said.

More Expedia customers are also booking through mobile devices, Khosrowshahi said. Most mobile customers are last-minute bookers, who instead of looking up at street hotel signs for deals — look down on their smartphones for mobile-exclusive rates and deals.

In addition to more mobile bookings, booking trends are rising for the holidays — though consumers are focused on value. Consumers are booking vacations, but shortening stays, for example, to five days from seven, Khosrowshahi said. "Consumers still travel. They adjust their patterns," he said.